6KWF
Crystal Structure Analysis of Endo-beta-1,4-xylanase II Complexed with Xylotriose
- PDB DOI: https://doi.org/10.2210/pdb6KWF/pdb
- Classification: HYDROLASE
- Organism(s): Trichoderma reesei RUT C-30
- Expression System: Escherichia coli
- Mutation(s): Yes 
- Deposited: 2019-09-06 Released: 2020-12-30 
- Funding Organization(s): National Natural Science Foundation of China
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.22 Å
- R-Value Free: 0.156 
- R-Value Work: 0.145 
- R-Value Observed: 0.145 
This is version 1.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Endo-1,4-beta-xylanase 2 | 190 | Trichoderma reesei RUT C-30 | Mutation(s): 1  Gene Names: xyn2, M419DRAFT_124931 EC: 3.2.1.8 | ||
UniProt | |||||
Find proteins for P36217 (Hypocrea jecorina (strain ATCC 56765 / BCRC 32924 / NRRL 11460 / Rut C-30)) Explore P36217  Go to UniProtKB:  P36217 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P36217 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
XYP (Subject of Investigation/LOI) Query on XYP | C [auth A] | beta-D-xylopyranose C5 H10 O5 SRBFZHDQGSBBOR-KKQCNMDGSA-N | |||
IOD (Subject of Investigation/LOI) Query on IOD | F [auth A], G [auth A], H [auth A], I [auth A] | IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M | |||
GOL (Subject of Investigation/LOI) Query on GOL | D [auth A], E [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_900117 Query on PRD_900117 | B | 4beta-beta-xylotriose | Oligosaccharide / Metabolism |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.22 Å
- R-Value Free: 0.156 
- R-Value Work: 0.145 
- R-Value Observed: 0.145 
- Space Group: I 2 2 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 66.679 | α = 90 |
b = 67.931 | β = 90 |
c = 78.81 | γ = 90 |
Software Name | Purpose |
---|---|
XDS | data reduction |
SCALEPACK | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
PHASER | phasing |
Entry History & Funding Information
Deposition Data
Funding Organization | Location | Grant Number |
---|---|---|
National Natural Science Foundation of China | China | 31670790 |
Revision History (Full details and data files)
- Version 1.0: 2020-12-30
Type: Initial release - Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description